Guide to Yeast Genetics: Functional Genomics, Proteomics, and Other Systems Analysis

PART I - Functional Genomics1. Analysis of Gene Function using DNA MicroarraysAndrew P. Capaldi2. An introduction to microarray data analysis and visualizationGregg B. Whitworth3. Genome-wide approaches to monitor pre-mRNA splicingMaki Inada and Jeff Pleiss4. ChIP-Seq: Using high-throughput DNA sequencing for genome-wide identification of transcription factor binding sitesPhilippe Lefrançois, Wei Zheng and Michael Snyder5. Genome-wide mapping of nucleosomes in yeastOliver J. Rando6. Genome-wide translational profiling by ribosome footprintingNicholas T. IngoliaPART II - Systematic Genetic Analysis7. Synthetic Genetic Array (SGA) Analysis in Saccharomyces cerevisiae and Schizosaccharomyces pombeAnastasia Baryshnikova, Michael Costanzo, Scott Dixon, Franco J. Vizeacoumar, Chad L. Myers, Brenda Andrews and Charles Boone8. Making temperature-sensitive mutantsShay Ben-Aroya, Xuewen Pan, Jef D. Boeke and Philip Hieter9. Quantitative Genetic Interaction Mapping using the E-MAP ApproachSean R. Collins, Assen Roguev and Nevan J. Krogan10. Exploring gene function and drug action using chemogenomic dosage assaysElke Ericson, Shawn Hoon, Robert P. St. Onge, Guri Giaever and Corey NislowPART III - Proteomics11. Yeast Expression Proteomics by High-Resolution Mass SpectrometryTobias C. Walther, Jesper V. Olsen and Matthias Mann12. High-quality binary interactome mappingMatija Dreze, Dario Monachello, Claire Lurin, Michael E. Cusick, David E. Hill, March Vidal, and Pascal Braun13. Quantitative analysis of protein phosphorylation on a system-wide scale by mass spectrometry based proteomicsBernd Bodenmiller and Rudi Aebersold14. A Toolkit of Protein-fragment Complementation Assays for Studying and Dissecting Large-scale and Dynamic Protein-Protein Interactions in Living CellsStephen W. Michnick, Po-Hien Ear, Christian Landry, Mohan K. Malleshaiah and Vincent Messier15. Yeast Lipid Analysis and Quantification by Mass SpectrometryXue Li Guan, Isabelle Riezman, Markus R. Wenk and Howard Riezman16. Mass Spectrometry-Based Metabolomics of YeastChristopher A. Crutchfield, Wenyun Lu, Eugene Melamud, and Joshua D. RabinowitzPART IV - Systems Analysis17. Imaging single mRNA molecules in yeastHyun Youk, Arjun Raj and Alexander van Oudenaarden18. Reconstructing gene histories in Ascomycota fungiIlanWapinski and Aviv Regev19. Experimental evolution in yeast: a practical guideMaitreya J. DunhamPART V - Synthetic Biology20. Enhancing stress resistance and production phenotypes through transcriptome engineeringFelix H. Lam, Franz S. Hartner, Gerald R. Fink, and Gregory StephanopoulosPART VI - Advances in Cytology/Biochemistry21. Visualizing yeast chromosomes and nuclear architecturePeter Meister, Lutz R. Gehlen, Elisa Varela, Veronique Kalck and Susan M. Gasser22. Quantitative localization of chromosomal loci by immunofluorescenceDonna Garvey Brickner, William Light and Jason H. Brickner23. Spinning Disk Confocal Microscopy of YeastKurt Thorn24. Correlative GFP-immunoelectron microscopy in yeastChristopher Buser and Kent McDonald25. Analyzing P-bodies and stress granules in Saccharomyces cerevisiaeJ Ross Buchan, Tracy Nissan and Roy Parker26. Analyzing mRNA expression using single mRNA resolution fluorescent in situ hybridizationDaniel Zenklusen and Robert H Singer27. The Use of In Vitro Assays to Measure Endoplasmic Reticulum Associated Degradation (ERAD)Jeffrey L. Brodsky28. A protein transformation protocol for introducing yeast prion particles into yeastMotomasa Tanaka29. Overexpression and Purification of Integral Membrane Proteins in YeastFranklin A. Hays, Zygy Roe-Zurz, and Robert M. Stroud30. Biochemical, cell biological and genetic assays to analyze amyloid and prion aggregation in yeastSimon Alberti, Randal Halfmann and Susan LindquistPART VII - Other Fungi31. Genetics and Molecular Biology in Candida albicansHernday, A.D., Noble, S. M., Mitrovich, Q.M., and Johnson, A.D.32. Molecular Genetics of Schizosaccharomyces pombeSarah A. Sabatinos and Susan L. Forsburg33. Applying Genetics and Molecular Biology to the Study of the Human Pathogen Cryptococcus neoformansCheryl D. Chun and Hiten D. Madhani34. The Fungal Genome Initiative and lessons learned from genome sequencingChristina A. Cuomo and Bruce W. Birren35. Ultradian metabolic cycles in yeastBenjamin Tu